title: Unsupervised automated high throughput phenotyping of RNAi time-lapse movies.
abstract: BACKGROUND
  Gene perturbation experiments in combination with fluorescence time-lapse cell imaging are a powerful tool in reverse genetics. High content applications require tools for the automated processing of the large amounts of data. These tools include in general several image processing steps, the extraction of morphological descriptors, and the grouping of cells into phenotype classes according to their descriptors. This phenotyping can be applied in a supervised or an unsupervised manner. Unsupervised methods are suitable for the discovery of formerly unknown phenotypes, which are expected to occur in high-throughput RNAi time-lapse screens.
  
  
  RESULTS
  We developed an unsupervised phenotyping approach based on Hidden Markov Models (HMMs) with multivariate Gaussian emissions for the detection of knockdown-specific phenotypes in RNAi time-lapse movies. The automated detection of abnormal cell morphologies allows us to assign a phenotypic fingerprint to each gene knockdown. By applying our method to the Mitocheck database, we show that a phenotypic fingerprint is indicative of a gene's function.
  
  
  CONCLUSIONS
  Our fully unsupervised HMM-based phenotyping is able to automatically identify cell morphologies that are specific for a certain knockdown. Beyond the identification of genes whose knockdown affects cell morphology, phenotypic fingerprints can be used to find modules of functionally related genes.
authors.affiliation: Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany. tresch@mpipz.mpg.de.
authors.forename: Henrik
authors.initials: H
authors.lastname: Failmezger
authors.forename: Holger
authors.initials: H
authors.lastname: Fröhlich
authors.forename: Achim
authors.initials: A
authors.lastname: Tresch
mesh_terms: D002460:Cell Line; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D055785:Gene Knockdown Techniques; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008853:Microscopy; D010641:Phenotype; D034622:RNA Interference; D059008:Time-Lapse Imaging / Q000379:methods*